20.20(S11):Advanced topics

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20.385: Advanced Topics in Synthetic Biology


Homework dropbox is here

Part 1: Readings

  • Paper 1 (10%)
  • Paper 2 (15%)
  • Response record (20%): your thoughts about the papers you don't present.
  • Participation in class discussions (5%): your thoughtful questions and ideas during the presentations of others

Instructions for these assignment are here

Part 2: Team Mentoring

  • Progress and Mentoring Reports (30%): one page summaries of your freshman team's work and dynamics
  • Team's project average (15%): based on the grade for the 3 major assignments submitted by your freshman team
  • Instructor Leverage (5%): discretionary adjustment by NK

Instructions for these assignments are here

Reading Schedule

Discussions will be 1 hour long during Wednesday 2-5 studio block


TOPIC DATE Discussion leader(s) Discussion paper(s) Related paper(s) to enjoy
Preview of 20.385 Wed Feb 2 Natalie Kuldell preview of 20.385 before next week read
  1. The promise of synthetic biology
  2. Two ‘What if' experiments
    Ptashne, M.
    PMID: 15055587
  3. Build Artificial
    Brent, R.
    PMID: 15055588
Parts™ Wed Feb 9 Natalie Kuldell
ppt is here
Turning lambda Cro into a transcriptional activatorBushman FD, Ptashne M.Cell. (1988) Jul 15;54(2):191-7.
PMID: 2968842
Improving the Lac System for Synthetic Biology
Penumetcha, P., et al. Bios (2011) 81(1):7-15.
Transcription-based Logic Devices
Wed Feb 16 Pei-Ann, Jessica
ppt is here
Environmental signal integration by a modular AND gate
Anderson JC, Voigt C, Arkin, AP Molecular systems biology (2007) 3:133
PMID: 17700541
A synthetic oscillatory network of transcriptional regulators
Elowitz, MB, and Leibler, S. Nature (2000) 403,

PMID: 10659856
Construction of a genetic toggle switch in Escherichia coli
Gardner TS, et al.Nature(2000) 403, 339–342
PMID: 10659857

Protein Design: directed evolution
Wed Feb 23 Yuan, Amber
ppt is here
De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth
Fisher MA, et al. PLoS One (2011)6(1):e15364
DOI: 10.1371/journal.pone.0015364
Directed evolution of recombinase specificity by split gene reassembly
Gersbach, CA, et al. NAR (2010) 38(12): 4198-4206-1543
DOI: 10.1093/nar/gkq125
RNA Engineering
Wed Mar 2 Andrew, Tina
ppt is here
Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins
Culler, SJ, Hoff, KG, Smolke, CD. Science (2010) 330:1251-1255
DOI: 10.1126/science.1192128
The Case for RNA
Chang, CL, Arkin AP. Science (2010) 330:1185-1186
DOI: 10.1126/science.1199495
Tuning the system: Network Composition
Wed Mar 10
before 3 ideas presentations, meet in 4-163
Colin, Raven
ppt is here
A modular positive feedback-based gene amplifier Nistala GJ et al. JBE (2010) 4:4
DOI: 10.1186/1754-1611-4-4
A fast, robust and tunable synthetic gene oscillator
Stricker, J. et al. Nature (2008) 456, 516–519
PMID: 18971928
(re)Programming Systems
Wed Mar 16 Patrick, Nick
ppt is here
Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA Warren L, et al. Cell Stem Cell (2010) 7:618-630
Reprogramming bacteria to seek and destroy an herbicide
Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470
Spring Break Mar 21-25 No class all week
DNA construction and editing technologies
Wed Mar 30 Raven, Andrew
Andrew's ppt is here
Raven's ppt is here
Programming cells by multiplex genome engineering and accelerated evolution
Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8.
PMID: 19633652
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides
Stemmer WP, et al. Gene (1995) 164(1):49-53
PMID: 7590320
Measurement technologies
Wed Apr 6
before tech spec review, meet in 56-114
ppt is here
Nascent transcript sequencing visualizes transcription at nucleotide resolutionChurchman LS and Weissman JS.Nature (2011)469:368-373 DOI: 10.1038/nature09652 Measuring the activity of BioBrick promoters using an in vivo reference standard
Kelly J, et al. Journal of Biological Engineering (2009) 3:4
Wed Apr 13 Jessica, Tina
Tina's ppt is here
Jessica will present next week
Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system
Shin J, and Noireaux, V. JBE (2010) 4:9
DOI: 10.1186/1754-1611-4-9
Emergent properties of reduced-genome Escherichia coli.
Pósfai G, et al. Science.(2006)312(5776):1044-6.
PMID: 16645050
Signal Connectivity
Wed Apr 20 Amber (will present Skerker paper next week)
Jessica's ppt is here
Rewiring the specificity of two-component signal transduction systems
Skerker JM, et al. Cell (2008)133(6):1043-54.
PMID: 18555780
Tunable Signal Processing in Synthetic MAP Kinase Cascades
O'Shaughnessy, EC, et al. Cell(2011) 144:119-131
DOI: 10.1016/j.cell.2010.12.014
Metabolic Engineering Wed Apr 27 Yuan
Amber's ppt is here
Yuan's ppt is here
Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.Moon TS et al. Metabolic Engineering (2010) 12: 298-305 (2010) PMID: 20117231 Production of the antimalarial drug precursor artemisinic acid in engineered yeast
Ro DK, et al. Nature (2006) 440, 940–943
PMID: 16612385
Cell Cell Communication/System Ecology Wed May 4 Colin
ppt is here
Robust multicellular computing using genetically encoded NOT gates and chemical 'wires'
Tamsir, a., Tabor, J.J., Voigt, C.A. Nature 2011 Jan 13;469:212-215.
DOI: 10.1038/nature09565
+ supplementary info
Division of logic labour
Li B and You L.Nature (2011) 469:171-172
Property rights in synthetic biology Wed May 11
before final presentations, meet in 56-114
ppt is here
Synthetic biology: caught between property rights, the public domain, and the commons
Rai A, Boyle J. PLoS Biol. (2007)5(3):e58
PMID: 17355173
Patents and Translational Research in Genomics
Kaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739.
Safety! Wed May 11
before final presentations, meet in 56-114
ppt is here
Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics.
Samuel GN, Selgelid MJ, Kerridge I. EMBO reports (2009) 10(1):7-11.
DOI: 10.1038/embor.2008.232
Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?
Michael Specter New Yorker article